CHANGES IN VERSION 1.3.3
-------------------------
NEW FEATURES
o updates in package vignette
BUG FIXES
o remove limitation of maximum typecode in the plot, now using rainbow()
CHANGES IN VERSION 1.3.2
-------------------------
BUG FIXES
o fix the returned posterior p
CHANGES IN VERSION 1.1.9
-------------------------
BUG FIXES
o NA bug when model fails
o using the length of the segment if shorter than maxk
CHANGES IN VERSION 1.1.8
-------------------------
NEW FEATURES
o add error catching in biomvRhsmm
o updates in package vignette
BUG FIXES
o fine tuning of memory usage for large count data structure
o minor bug fixes
CHANGES IN VERSION 1.1.7
-------------------------
NEW FEATURES
o add support of Rle like sparse data in mcols of large count data structure.
o add mclapply for parallel processing of different seqnames in biomvRhsmm
CHANGES IN VERSION 1.1.6
-------------------------
BUG FIXES
o fix nbinom emis estimateSegCommonDisp -> nbinomCLLDD
CHANGES IN VERSION 1.1.5
-------------------------
NEW FEATURES
o update biomvRGviz to have trackList returned when tofile=FALSE
BUG FIXES
o typo fix in function argument
CHANGES IN VERSION 1.1.4
-------------------------
NEW FEATURES
o update biomvRGviz to plot multiple samples in one, and more param
o plot method now defaults to multiple samples in one, sampleInOne=T
BUG FIXES
o fix states rank when prior.m=cluster
CHANGES IN VERSION 1.1.3
-------------------------
NEW FEATURES
o the x slot in the returning object for biomvRhsmm now also contains the probability of associated state for each position
o the param slot in the returning object for biomvRhsmm now also contains the updated emission and sojourn parameters for each seqname and sample column
CHANGES IN VERSION 1.1.2
-------------------------
NEW FEATURES
o add a new clustering method for emission prior estimation
o add a new example section of DMR detection in the vignette
BUG FIXES
o switch off several data checking warnings, use normal cat() instead
CHANGES IN VERSION 1.1.1
-------------------------
NEW FEATURES
o add support of direct input of sojourn parameters as named list.
BUG FIXES
o suppress warnings generated when appending GRanges object for the output
CHANGES IN VERSION 0.99.3
-------------------------
NEW FEATURES
o add mvt and t to the emis.type and tmvtFit function
BUG FIXES
o fix shift index (-1) in pois and nbinom fitting
CHANGES IN VERSION 0.99.2
-------------------------
NEW FEATURES
o add log-Vertibi in c
o add normalizing factor for estimation of emis$p and soj$d
o add avgFunc to be used in average calculation, median and mean with trim, default to median
BUG FIXES
o fix shift index (-1) in pois and nbinom fitting
CHANGES IN VERSION 0.99.1
-------------------------
NEW FEATURES
o in Bioc-devel